PROJECT SUMMARY

Recurrent change-of-function mutations in RNA splicing factors are highly prevalent in MDS and related myeloid neoplasms and represent clear drivers of disease. Our group previously demonstrated that cells bearing heterozygous mutations in MDS-associated RNA splicing factors are unable to sustain any further genetic or pharmacologic perturbations to the RNA splicing process; however, finding drugs that can safely and effectively inhibit splicing in cancer cells without causing toxicity to normal cells has been a barrier to translation. We recently systematically interrogated RNA-binding protein (RBP) dependencies in human cancers using a comprehensive CRISPR/Cas9 domain-focused screen targeting RNA-binding domains (RBDs) of 490 classical RBPs. Genetic or pharmacologic targeting of one key member of this network, RBM39, repressed cassette exon inclusion and promoted intron retention within mRNAs encoding HOXA9 targets as well as in other RBPs required in myeloid neoplasms. The effects of RBM39 loss on splicing further resulted in preferential lethality of spliceosomal mutant malignancies.

Overall these data identify RBM39 as central to a network of functionally and physically interacting RBPs upregulated in myeloid malignancies over normal hematopoietic precursors. Despite these insights we do not yet understand the basis for the cell- and context-specific roles of RBM39 in malignant versus normal hematopoietic cells. We also do not know the therapeutic potential of this approach in actual MDS patients. We hypothesize that RBM39 is differentially required in malignant versus normal hematopoietic cells, may be differentially required depending on the precise stage of normal hematopoiesis, and will be a therapeutic target for spliceosomal mutant myeloid neoplasms.